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Research: Experimental and pan-cancer genome analyses reveal widespread contribution of acrylamide exposure to carcinogenesis in humans
- Maria Zhivagui,
- Alvin W.T. Ng,
- Maude Ardin,
- Mona I. Churchwell,
- Manuraj Pandey,
- Claire Renard,
- Stephanie Villar,
- Vincent Cahais,
- Alexis Robitaille,
- Liacine Bouaoun,
- Adriana Heguy,
- Kathryn Z. Guyton,
- Martha R. Stampfer,
- James McKay,
- Monica Hollstein,
- Magali Olivier,
- Steven G. Rozen,
- Frederick A. Beland,
- Michael Korenjak,
- and Jiri Zavadil
Genome Res. April 2019 29: 521-531; Published in Advance March 7, 2019, doi:10.1101/gr.242453.118
...Experimental and pan-cancer analyses reveal widespread contribution of acrylamide exposure to carcinogenesis in humans Maria Zhivagui1, Alvin W.T. Ng2,3,4, Maude Ardin1, Mona I. Churchwell5, Manuraj Pandey1, Claire Renard1, Stephanie Villar1, Vincent Cahais6, Alexis Robitaille7, Liacine Bouaoun8...
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Perspective: Constructing genomic maps of positive selection in humans: Where do we go from here?
- Joshua M. Akey
Genome Res. May 2009 19: 711-722; doi:10.1101/gr.086652.108
...models, would be invaluable for guiding efficient study designs in -wide scans of selection. In summary, -wide analyses of positive selection described to date suggest widespread signatures of positive selection in the human . Although these newly constructedmaps of selection likely include genuine...
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Method: Gene duplication is associated with gene diversification and potential neofunctionalization in lung cancer evolution
- Paul Ashford,
- Alexander M. Frankell,
- Zofia Piszka,
- Camilla S.M. Pang,
- Mahnaz Abbasian,
- Maise Al Bakir,
- Mariam Jamal-Hanjani,
- Nicholas McGranahan,
- Charles Swanton,
- and Christine A. Orengo
Genome Res. March 2026 36: 561-577; Published in Advance February 19, 2026, doi:10.1101/gr.278663.123
...Group, Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London WC1E 6DD, United Kingdom Corresponding author: c.orengo@ucl.ac.ukAbstractTumors evolve through a process of selection on somatic mutations, driving cell division and tissue growth through...
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Research: Convergent relaxation of molecular constraint in herbivores reveals the changing role of liver and kidney functions across mammalian diets
- Matthew D. Pollard,
- Wynn K. Meyer,
- and Emily E. Puckett
Genome Res. December 2024 34: 2176-2189; Published in Advance November 22, 2024, doi:10.1101/gr.278930.124
....Carnivore-specific positive selection acting on O-linked glycosylation pathways and metalloprotease activity may have relevance to human diabetes. Enrichment for these pathways was primarily driven by four ADAMTS genes. O-linked glycosylation is a widespread posttranslational modification of ADAMTS metalloproteases (Wang et...
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Research: Genomic analyses provide insights into peach local adaptation and responses to climate change
- Yong Li,
- Ke Cao,
- Nan Li,
- Gengrui Zhu,
- Weichao Fang,
- Changwen Chen,
- Xinwei Wang,
- Jian Guo,
- Qi Wang,
- Tiyu Ding,
- Jiao Wang,
- Liping Guan,
- Junxiu Wang,
- Kuozhan Liu,
- Wenwu Guo,
- Pere Arús,
- Sanwen Huang,
- Zhangjun Fei,
- and Lirong Wang
Genome Res. April 2021 31: 592-606; Published in Advance March 9, 2021, doi:10.1101/gr.261032.120
..., members of which provide one of the world's main resources of fruits. Peach originated in southwestern China, and its landraces and wild relatives are widespread in both temperate and subtropical regions, as well as in wet and dry climates (Wang et al. 2012). Moreover, peach and its wild relatives can...
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Resource: The Drosophila brain on cocaine at single-cell resolution
- Brandon M. Baker,
- Sneha S. Mokashi,
- Vijay Shankar,
- Jeffrey S. Hatfield,
- Rachel C. Hannah,
- Trudy F.C. Mackay,
- and Robert R.H. Anholt
Genome Res. October 2021 31: 1927-1937; Published in Advance May 25, 2021, doi:10.1101/gr.268037.120
...and development of preference for these psychostimulants (Highfill et al. 2019). However, RNAi-mediated reduction in expression of candidate genes in glia also affected cocaine consumption, suggesting that widespread brain regions contribute to cocaine-associated behavioral phenotypes. The present study aims...
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Review: Contrasting genetic architectures in different mouse reference populations used for studying complex traits
- David A. Buchner and
- Joseph H. Nadeau
Genome Res. June 2015 25: 775-791; Published in Advance May 7, 2015, doi:10.1101/gr.187450.114
...functions, and systems properties that underlie phenotypic variation and disease risk in humans, model organisms, agricultural species, and natural populations. The challenges are many, beginning with the seemingly simple tasks of mapping QTLs and identifying their underlying genetic determinants. Various...
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Research: Integrative phenomics reveals insight into the structure of phenotypic diversity in budding yeast
- Daniel A. Skelly,
- Gennifer E. Merrihew,
- Michael Riffle,
- Caitlin F. Connelly,
- Emily O. Kerr,
- Marnie Johansson,
- Daniel Jaschob,
- Beth Graczyk,
- Nicholas J. Shulman,
- Jon Wakefield,
- Sara J. Cooper,
- Stanley Fields,
- William S. Noble,
- Eric G.D. Muller,
- Trisha N. Davis,
- Maitreya J. Dunham,
- Michael J. MacCoss,
- and Joshua M. Akey
Genome Res. September 2013 23: 1496-1504; Published in Advance May 29, 2013, doi:10.1101/gr.155762.113
...in a model organism with complex and heterogeneous patterns of population structure. Pervasive phenotypic diversity We found widespread heritable variation within every class of phenotypic data measured, with >50% of all measured traits varying between strains. Specifically, 74% (4565) of transcript levels...
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Method: High-throughput profiling of amino acids in strains of the Saccharomyces cerevisiae deletion collection
- Sara J. Cooper,
- Gregory L. Finney,
- Shauna L. Brown,
- Sven K. Nelson,
- Jay Hesselberth,
- Michael J. MacCoss,
- and Stanley Fields
Genome Res. September 2010 20: 1288-1296; Published in Advance July 7, 2010, doi:10.1101/gr.105825.110
...TR, Roberts CJ, Dai H, Jones AR,MeyerMR, SladeD, Burchard J, Dow S, Ward TR, Kidd MJ, et al. 2000. Widespread aneuploidy revealed by DNA microarray expression profiling. Nat Genet 25: 333–337. HuhWK, Falvo JV, Gerke LC, Carroll AS, Howson RW,Weissman JS, O’Shea EK. 2003. Global analysis of protein...
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Research: Evolution at two levels of gene expression in yeast
- Carlo G. Artieri and
- Hunter B. Fraser
Genome Res. March 2014 24: 411-421; Published in Advance December 6, 2013, doi:10.1101/gr.165522.113
...a comprehensive view of gene expression evolution Although we have discovered widespread natural selection contributing to the divergence of translation rates, complementing the extensive literature on the evolution of mRNA abundances, these two levels still represent only a fraction of the steps from DNA...

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